Is there any way I can perform the above?

Not particularly efficient, but possible:

$s = '1 AC2 34 TRP A 6 ALA A 7 ILE A 14 GLY A 15';;

print for grep length, split /(\S+\s+\S+\s+\S+)\s+/, $s;;
1 AC2 34
TRP A 6
ALA A 7
ILE A 14
GLY A 15
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